Separating the crossovers out of the main deck only takes a couple of minutes at the end, it's not that time consuming IMO.

Would also recommend against playing *just* the crossovers mashed together. The mechanics between them are vastly different (Time Travel, card rotation, Teamwork, etc.) and would make for a very cumbersome, unwieldy game. But like Lex said, it's your game and there's nothing stopping you. Give it a shot and see if you like it.

I also favor custom main decks. There's a good thread from one of the developers, StormKing, where he lists his favorite Watchmen decklist. I have a Batman/Gotham deck and love to deckbuild around themes or even favorite cards. Not easy to unmix, but when you create the right mix it can become your go-to('s).

I actually mixed the 1st and 2nd Base sets (2012+2013) with Crisis 1 and Crisis 2. It came out great. I took out the boring cards the red martian cards and harley quinn (make everyone discard if u play 3) I took out alot of Extra VP cards like utility belt (those ones that give you 5vp or more for owning heroes/equips/etc. I limited them to like 2 or 3 specific cards (like the power rings). I made it so that deck thinning was more possible. Destruction cards are somewhat heavy like Nth Metal and Red lantern corps, Aquaman's 5 cost card, Cards that destroy cards in your hand, discard pile (Heatray Vision) Bulletproof (defense). I use this deck the most.

Just pay attention to the original balance of cards (in a base set) Heroes/equips/villains/superpowers. Super powers are the least by a safe margin. My main deck has expanded to 120-125 cards. There is a 7 cost card of just about every card type. Super Strength (SP) Starro(Villain) Ganthet (hero), Super Strength (hero) and I forget the equipment one (White Lantern Battery charger?).

I took out vanilla cards like The Flash (cost 2, draw a card(set 1) and Legion Flight Ring ((set 2)cost 2 draw a card) for Raven's cost 3 - draw a card and +1.